Article
Genetics & Heredity
Logan S. Whitehouse, Daniel R. Schrider
Summary: Timesweeper is a convolutional neural network-based tool that can identify selective sweeps using continuous genomic time-series data. It demonstrates that more accurate inferences about natural selection can be made using genomic time-series data.
Article
Evolutionary Biology
Ying Guo, Jen-Hsiang Ou, Yanjun Zan, Yuzhe Wang, Huifang Li, Chunhong Zhu, Kuanwei Chen, Xin Zhou, Xiaoxiang Hu, Orjan Carlborg
Summary: The study evaluated the genomic structure and diversity of worldwide chicken breeds, studying divergence from selection and historical admixture events. Results showed that modern chicken stocks for meat production in both Asian and Western agriculture are dominated by contributions from heavy Asian breeds, with confirmed connections to functional genes for feather coloring.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Shaohua Fan, Jeffrey P. Spence, Yuanqing Feng, Matthew E. B. Hansen, Jonathan Terhorst, Marcia H. Beltrame, Alessia Ranciaro, Jibril Hirbo, William Beggs, Neil Thomas, Thomas Nyambo, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Alfred Njamnshi, Charles Folkunang, Dawit Wolde Meskel, Gurja Belay, Yun S. Song, Sarah A. Tishkoff
Summary: By conducting whole-genome sequencing of indigenous African populations, we identified numerous unreported variants and observed evidence of ancient population structure and introgression events from highly diverged ''ghost'' populations. We also found signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes.
Editorial Material
Microbiology
Nandita Garud
Summary: Microbes can evolve rapidly to adapt to selection pressures, but our understanding of the adaptation in microbiomes is still incomplete. Advances in modeling complex populations and scenarios will help us better understand adaptation in microbiomes and other natural populations experiencing similar complexities.
Article
Genetics & Heredity
Pablo Villegas-Miron, Sandra Acosta, Jessica Nye, Jaume Bertranpetit, Hafid Laayouni
Summary: Recent positive selection events on the X chromosome in human populations show a higher number among sub-Saharan Africans compared to non-African populations. A global enrichment of neural-related processes and the importance of fertility-related genes in human evolution are observed. Commonalities in genes across different continental groups, as well as signals in genes that escape X chromosome inactivation, are reported.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Y. Steyn, T. Lawlor, Y. Masuda, S. Tsuruta, A. Legarra, D. Lourenco, I. Misztal
Summary: Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. Stratifying selected candidates into sub-populations using K-means clustering successfully separated genetically different groups.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Biology
Einar Arnason, Jere Koskela, Katrin Halldorsdottir, Bjarki Eldon
Summary: Highly fecund natural populations with high early mortality have limited understanding of their recruitment dynamics. The concept of sweepstakes reproductive success, which involves variance and skew in individual reproductive output, is key to understanding individual reproductive success distribution. It is still unclear whether highly fecund organisms reproduce through sweepstakes and the relative roles of neutral and selective sweepstakes.
Article
Genetics & Heredity
Santiago G. Medina-Munoz, Diego Ortega-Del Vecchyo, Luis Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Lourdes Garcia-Garcia, Andres Moreno-Estrada, Aaron P. Ragsdale
Summary: This study used high-coverage whole-genome data and existing genomes from Latin America to infer the complex evolutionary history of Latin American populations. The models developed in this study provide a more accurate prediction of genetic variation in admixed populations and can be a valuable resource for future studies.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Maike L. Morrison, Nicolas Alcala, Noah A. Rosenberg
Summary: In model-based inference of population structure, individuals are assigned membership coefficients in statistical clusters generated by clustering algorithms. Different groups of individuals can have distinct patterns of variability in their membership coefficients, which are difficult to capture using a single numerical value. We introduce a method that measures the variability of membership coefficients in a predefined group, using an analogy between individual membership coefficient vectors and population allele frequency vectors. Our approach makes use of a normalized F-ST statistic and can be used to compare and analyze inferred population structures.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Alexander T. Xue, Daniel R. Schrider, Andrew D. Kern
Summary: The partialS/HIC method utilizes deep learning to identify ongoing selective sweeps in population genomic data, demonstrating excellent performance in distinguishing between various types of sweeps under different demographic scenarios. Applied to real mosquito populations exposed to insecticides, the tool reveals an overrepresentation of sweeps at insecticide resistance loci, providing potential candidate loci for mosquito control efforts. This supervised machine learning approach introduces a valuable tool for tracking ongoing evolutionary dynamics in the rapidly accumulating whole-genome data of diverse organisms.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Michael Dannemann
Summary: Research has found associations between Neandertal-derived DNA and autoimmune diseases, prostate cancer, and type 2 diabetes, with many of these disease associations linked to specific populations' Neandertal DNA.
GENOME BIOLOGY AND EVOLUTION
(2021)
Review
Agriculture, Dairy & Animal Science
Sumaya Kambal, Abdulfatai Tijjani, Sabah A. E. Ibrahim, Mohamed-Khair A. Ahmed, Joram M. Mwacharo, Olivier Hanotte
Summary: The review summarizes the research on genomic regions under positive selection in indigenous African cattle breeds, highlighting candidate genes and genome regions associated with adaptation to extreme environments and environmental challenges such as heat stress, infectious diseases, and high altitude. The review also emphasizes the importance of identifying candidate causative variants controlling these traits and provides guidance for future targeted genome studies. The highest numbers of candidate regions are found on BTA3, BTA5, and BTA7, overlapping with genes involved in various biological functions and pathways.
Review
Biology
Shyamalika Gopalan, Samuel Pattillo Smith, Katharine Korunes, Iman Hamid, Sohini Ramachandran, Amy Goldberg
Summary: Geneticists have made significant progress in understanding human genetic diversity, particularly in the field of admixture population genetics. Admixture is an important evolutionary process that affects genetic variation and evolution between populations. Overcoming limitations in studying admixed populations using traditional methods, researchers have leveraged genomic signatures to gain insights into human history, natural selection, and complex trait architecture.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Huashui Ai, Mingpeng Zhang, Bin Yang, Amy Goldberg, Wanbo Li, Junwu Ma, Debora Brandt, Zhiyan Zhang, Rasmus Nielsen, Lusheng Huang
Summary: Research on Eurasian pig populations revealed significant genetic haplotype differences and hybridization history. By analyzing Y chromosome data, the study uncovered three distinct waves of European gene introgression into Asian pig populations in the last 200 years, as well as the presence and distribution of European Y chromosomes in Chinese pig breeds. The European Y haplotype in Chinese pigs is associated with lean meat production, suggesting artificial selection as a driving force for its increased frequency.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Alison F. Feder, Pleuni S. Pennings, Dmitri A. Petrov
Summary: This paper demonstrates the use of time series data to bound evolutionary parameters, complementing and informing traditional population genetic approaches. By studying drug-induced resistance evolution in HIV, we show new evidence that early HIV treatment failure was driven by soft sweeps.
Article
Biochemical Research Methods
Lenore Pipes, Rasmus Nielsen
Summary: The study developed a phylogenetic clustering method called AncestralClust for clustering divergent sequences. Comparison with other state-of-the-art clustering methods showed that AncestralClust has higher accuracy and more even cluster sizes in divergent datasets.
Article
Biochemical Research Methods
Sandra Hui, Rasmus Nielsen
Summary: This study introduces a theoretical framework to accurately call CNAs using tumor evolutionary history, developing a method called SCONCE to analyze read depth data from tumor cells which accurately decodes copy number profiles and provides a useful tool for understanding tumor evolution.
Article
Biology
Geno Guerra, Rasmus Nielsen
Summary: The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. This study derived and implemented exact expressions for the covariances of pairwise coalescence times under phylogenetic models with piecewise constant changes in population size. It also derived approximations for the expectation and bias of a sequence-based estimator of F-ST and showed that the estimator is generally biased downward.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Genetics & Heredity
Debora Y. C. Brandt, Xinzhu Wei, Yun Deng, Andrew H. Vaughn, Rasmus Nielsen
Summary: This study compared the estimates of coalescence times from three ancestral recombination graph inference programs using standard neutral coalescent simulations. The results showed that ARGweaver had the most accurate estimates at each locus, while Relate was often more accurate than tsinfer+tsdate. However, all three methods tended to overestimate small coalescence times and underestimate large ones. The posterior distribution of ARGweaver was closer to the expected distribution compared to Relate, but it sacrificed scalability.
Article
Evolutionary Biology
Yuanting Jin, Diana Aguilar-Gomez, Debora Y. C. Brandt, Tyler A. Square, Jiasheng Li, Zhengxia Liu, Tao Wang, Peter H. Sudmant, Craig T. Miller, Rasmus Nielsen
Summary: This study analyzed the genome of the variegated toad-headed agama and found that substrate color plays an important role in the melanism adaptation of the lizard.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Mason Liang, Mikhail Shishkin, Anastasia Mikhailova, Vladimir Shchur, Rasmus Nielsen
Summary: Estimating admixture histories is crucial for understanding genetic diversity. A new statistical method based on analytical expressions for expected ALD in a three-locus system has been developed to resolve more complicated admixture histories.
Review
Biochemical Research Methods
Dylan Feldner-Busztin, Panos Firbas Nisantzis, Shelley Jane Edmunds, Gergely Boza, Fernando Racimo, Shyam Gopalakrishnan, Morten Tonsberg Limborg, Leo Lahti, Gonzalo G. de Polavieja
Summary: Motivated by the need to automate information extraction from large datasets, machine learning methods are employed for integrative joint analysis of diverse omics data. A systematic assessment of the literature reveals the widespread use of dimensionality reduction methods and models that can handle datasets with limited samples. The Cancer Genome Atlas dataset has a significant impact on the field.
Letter
Multidisciplinary Sciences
Yucheng Wang, Ana Prohaska, Haoran Dong, Adriana Alberti, Inger Greve Alsos, David W. Beilman, Anders A. Bjork, Jialu Cao, Anna A. Cherezova, Eric Coissac, Bianca De Sanctis, France Denoeud, Christoph Dockter, Richard Durbin, Mary E. Edwards, Neil R. Edwards, Julie Esdale, Grigory B. Fedorov, Antonio Fernandez-Guerra, Duane G. Froese, Galina Gusarova, James Haile, Philip B. Holden, Kristian K. Kjeldsen, Kurt H. Kjaer, Thorfinn Sand Korneliussen, Youri Lammers, Nicolaj Krog Larsen, Ruairidh Macleod, Jan Mangerud, Hugh McColl, Marie Kristine Foreid Merkel, Daniel Money, Per Moller, David Nogues-Bravo, Ludovic Orlando, Hannah Lois Owens, Mikkel Winther Pedersen, Fernando Racimo, Carsten Rahbek, Jeffrey T. Rasic, Alexandra Rouillard, Anthony H. Ruter, Birgitte Skadhauge, John Inge Svendsen, Alexei Tikhonov, Lasse Vinner, Patrick Wincker, Yingchun Xing, Yubin Zhang, David J. Meltzer, Eske Willerslev
Article
Biology
Rasa A. Muktupavela, Martin Petr, Laure Segurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo
Summary: Ancient genome sequencing technologies allow us to study natural selection in unprecedented detail by directly observing the presence or absence of specific alleles in a particular region during the last 10,000 years. However, a complete understanding of natural selection requires more nuanced statistical methods to model allele frequency changes across space and time.
Editorial Material
Biology
Fernando Racimo, Elia Valentini, Gaston Rijo De Leon, Teresa L. Santos, Anna Norberg, Lane M. Atmore, Myranda Murray, Sanja M. Hakala, Frederik Appel Olsen, Charlie J. Gardner, Julia B. Halder
Summary: Our current economic and political structures are causing an increasingly devastating impact on the Earth's climate and ecosystems, leading to a biospheric emergency with catastrophic consequences. Life scientists have a crucial role in documenting this emergency, but they need to engage in advocacy and activism to urge governments to take action and drive systemic change. Scientists are urged to participate in nonviolent civil resistance, a proven effective form of public engagement in social struggles.
Article
Biochemistry & Molecular Biology
Bjort K. Kragesteen, Amir Giladi, Eyal David, Shahar Halevi, Laufey Geirsdottir, Olga M. Lempke, Baoguo Li, Andreas M. Bapst, Ken Xie, Yonatan Katzenelenbogen, Sophie L. Dahl, Fadi Sheban, Anna Gurevich-Shapiro, Mor Zada, Truong San Phan, Roberto Avellino, Shuang-Yin Wang, Oren Barboy, Shir Shlomi-Loubaton, Sandra Winning, Philipp P. Markwerth, Snir Dekalo, Hadas Keren-Shaul, Merav Kedmi, Martin Sikora, Joachim Fandrey, Thorfinn S. Korneliussen, Josef T. Prchal, Barak Rosenzweig, Vladimir Yutkin, Fernando Racimo, Eske Willerslev, Chamutal Gur, Roland H. Wenger, Ido Amit
Summary: Single-cell RNA and transposase-accessible chromatin (ATAC) sequencing in a mouse model identified a rare cell subset called Norn cells in kidney stroma as the major source of endocrine Epo production in mice, and this finding was confirmed in human kidney tissues. These findings provide new insights into EPO gene regulation and may lead to improved therapies for anemia.
Article
Ecology
Joana L. Rocha, Pedro Silva, Nuno Santos, Monia Nakamura, Sandra Afonso, Abdeljebbar Qninba, Zbyszek Boratynski, Peter H. Sudmant, Jose C. Brito, Rasmus Nielsen, Raquel Godinho
Summary: Analysis of whole genomes of four fox species shows that introgression facilitated adaptation to the hot arid environment of the Sahara Desert and suggests renal water homeostasis as a mechanism of adaptation in the extreme desert specialist species.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Marie Louis, Petra Korlevic, Milaja Nykanen, Frederick Archer, Simon Berrow, Andrew Brownlow, Eline D. Lorenzen, Joanne O'Brien, Klaas Post, Fernando Racimo, Emer Rogan, Patricia E. Rosel, Mikkel-Holger S. Sinding, Henry van der Es, Nathan Wales, Michael C. Fontaine, Oscar E. Gaggiotti, Andrew D. Foote
Summary: Parallel evolution provides evidence of adaptation to local environmental variation through natural selection. By comparing mid-Holocene and contemporary bottlenose dolphin genomes, the study reveals a stronger correlation between dolphins and coastal populations as the samples become more recent. The analysis suggests that coastal-associated genetic variants increased in frequency when coastal habitats emerged, and that the rapid adaptation to these habitats was facilitated by shared genetic variation between pelagic and coastal populations. The findings shed light on the chronology and mode of parallel evolution, contributing to our understanding of how species adapt to new environments.
NATURE COMMUNICATIONS
(2023)
Article
Engineering, Biomedical
Hanqin Li, Rebecca Bartke, Lei Zhao, Yogendra Verma, Anna Horacek, Alma Rechav Ben-Natan, Gabriella R. R. Pangilinan, Netravathi Krishnappa, Rasmus Nielsen, Dirk Hockemeyer
Summary: By deleting one copy of the BRCA2 gene, human pluripotent stem cells can be used to annotate gene variants and test their sensitivity to poly(ADP-ribose) polymerase inhibition. Mutations in the BRCA2 gene are associated with sporadic and familial cancer, causing genomic instability and sensitizing cancer cells to poly(ADP-ribose) polymerase inhibition. The deletion of one copy of BRCA2 in human pluripotent stem cells allows for detailed characterization of essential regions in the gene and evaluation of clinical BRCA2 variants' sensitivity to poly(ADP-ribose) polymerase inhibitors.
NATURE BIOMEDICAL ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Jennifer R. S. Meadows, Jeffrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laurent A. F. Frantz, Meharji Arumilli, Sruthi Hundi, Kerstin Lindblad-Toh, Catarina Ginja, Kadek Karang Agustina, Catherine Andre, Adam R. Boyko, Brian W. Davis, Michaela Droegemueller, Xin-Yao Feng, Konstantinos Gkagkavouzis, Giorgos Iliopoulos, Alexander C. Harris, Marjo K. Hytonen, Daniela C. Kalthoff, Yan-Hu Liu, Petros Lymberakis, Nikolaos Poulakakis, Ana Elisabete Pires, Fernando Racimo, Fabian Ramos-Almodovar, Peter Savolainen, Semina Venetsani, Imke Tammen, Alexandros Triantafyllidis, Bridgett vonHoldt, Robert K. Wayne, Greger Larson, Frank W. Nicholas, Hannes Lohi, Tosso Leeb, Ya-Ping Zhang, Elaine A. Ostrander
Summary: The international Dog10K project aims to sequence and analyze thousands of canine genomes, and has discovered a high percentage of genomic variation across 239 sampled breeds. The project has also identified retrogene insertions from 926 parent genes. These findings are crucial for studying domestication, behavior, morphology, disease susceptibility, and genome architecture and function.